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Academic Journal

Dissecting gene expression networks in the developing hippocampus through the lens of NEIL3 depletion.

  • Authors : Bugaj AM; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.; Kunath N

Subjects: Gene Expression Regulation* ; Gene Regulatory Networks*/Gene Regulatory Networks*/Gene Regulatory Networks*/genetics; Animals

  • Source: Progress in neurobiology [Prog Neurobiol] 2024 Apr; Vol. 235, pp. 102599. Date of Electronic Publication: 2024 Mar 24.Publisher: Pergamon Press Country of Publication: England NLM ID: 0370121 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

voyAGEr, a free web interface for the analysis of age-related gene expression alterations in human tissues.

  • Authors : Schneider AL; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.; Martins-Silva R

Subjects: Transcriptome* ; Gene Expression Profiling*; Humans

  • Source: ELife [Elife] 2024 Mar 28; Vol. 12. Date of Electronic Publication: 2024 Mar 28.Publisher: eLife Sciences Publications, Ltd Country of Publication: England NLM ID: 101579614 Publication Model: Electronic Cited Medium: Internet

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Academic Journal

Reliable reference gene selection for quantitative real-time PCR (qRT-PCR) in floral developmental phases of dioecious species Coccinia grandis.

Subjects: Gene Expression Regulation, Plant* ; Cucurbitaceae*/Cucurbitaceae*/Cucurbitaceae*/genetics; Real-Time Polymerase Chain Reaction

  • Source: Gene [Gene] 2024 Mar 30; Vol. 900, pp. 148143. Date of Electronic Publication: 2024 Jan 07.Publisher: Elsevier/North-Holland Country of Publication: Netherlands NLM ID: 7706761 Publication Model: Print-Electronic Cited Medium: Internet

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Academic Journal

A Data-Distribution and Successive Spline Points based discretization approach for evolving gene regulatory networks from scRNA-Seq time-series data using Cartesian Genetic Programming.

Subjects: Gene Regulatory Networks*/Gene Regulatory Networks*/Gene Regulatory Networks*/genetics ; Single-Cell Gene Expression Analysis* ; Tosyl Compounds*

  • Source: Bio Systems [Biosystems] 2024 Feb; Vol. 236, pp. 105126. Date of Electronic Publication: 2024 Jan 24.Publisher: Elsevier Science Ireland Country of Publication: Ireland NLM ID: 0430773 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq.

  • Authors : Fan Y; Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China.; Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region

Subjects: Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods ; Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: Genome biology [Genome Biol] 2024 Apr 15; Vol. 25 (1), pp. 96. Date of Electronic Publication: 2024 Apr 15.Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

The Web-Based Portal SpatialTME Integrates Histological Images with Single-Cell and Spatial Transcriptomics to Explore the Tumor Microenvironment.

  • Authors : Shi J; Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.; Wei X

Subjects: Tumor Microenvironment*/Tumor Microenvironment*/Tumor Microenvironment*/genetics ; Gene Expression Profiling*; Humans

  • Source: Cancer research [Cancer Res] 2024 Apr 15; Vol. 84 (8), pp. 1210-1220.Publisher: American Association for Cancer Research Country of Publication: United States NLM ID: 2984705R Publication Model: Print Cited Medium:

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Academic Journal

Transcriptome profiling of aerial and subterranean peanut pod development.

  • Authors : Peng Z; Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.; Jia KH

Subjects: Arachis*/Arachis*/Arachis*/genetics ; Arachis*/Arachis*/Arachis*/growth & development ; Gene Expression Regulation, Plant*

  • Source: Scientific data [Sci Data] 2024 Apr 11; Vol. 11 (1), pp. 364. Date of Electronic Publication: 2024 Apr 11.Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101640192 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq.

  • Authors : Fishman L; Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel.; Modak A

Subjects: Zebrafish* ; Single-Cell Gene Expression Analysis*; Animals

  • Source: Nature communications [Nat Commun] 2024 Apr 10; Vol. 15 (1), pp. 3104. Date of Electronic Publication: 2024 Apr 10.Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.

  • Authors : Eisele AS; Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland. .; Tarbier M

Subjects: Gene Expression Profiling* ; Software*; Humans

  • Source: Nature communications [Nat Commun] 2024 Mar 29; Vol. 15 (1), pp. 2744. Date of Electronic Publication: 2024 Mar 29.Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells.

  • Authors : Jiang A; Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand.; Snell RG

Subjects: Algorithms* ; Single-Cell Gene Expression Analysis*; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Mar 29; Vol. 40 (4).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

Multi-organ single-cell transcriptomics of immune cells uncovered organ-specific gene expression and functions.

Subjects: Gene Expression Profiling* ; Transcriptome* ; Immune System*/Immune System*/Immune System*/cytology

  • Source: Scientific data [Sci Data] 2024 Mar 27; Vol. 11 (1), pp. 316. Date of Electronic Publication: 2024 Mar 27.Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101640192 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

Reference Genes Selection and Validation for Cinnamomum burmanni by Real-Time Quantitative Polymerase Chain Reaction.

  • Authors : Shi L; College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China.; Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China.

Subjects: Gene Expression Regulation, Plant* ; Cinnamomum*/Cinnamomum*/Cinnamomum*/genetics; Sodium Chloride

  • Source: International journal of molecular sciences [Int J Mol Sci] 2024 Mar 20; Vol. 25 (6). Date of Electronic Publication: 2024 Mar 20.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Academic Journal

An improved hierarchical variational autoencoder for cell-cell communication estimation using single-cell RNA-seq data.

  • Authors : Liu S; School of Computer Science, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, China.; Zhang Y

Subjects: Single-Cell Gene Expression Analysis* ; Neoplasms*; Humans

  • Source: Briefings in functional genomics [Brief Funct Genomics] 2024 Mar 20; Vol. 23 (2), pp. 118-127.Publisher: Oxford University Press Country of Publication: England NLM ID: 101528229 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies.

  • Authors : Guo X; School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China.; Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China.

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: Briefings in functional genomics [Brief Funct Genomics] 2024 Mar 20; Vol. 23 (2), pp. 95-109.Publisher: Oxford University Press Country of Publication: England NLM ID: 101528229 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

Single-cell RNA-seq revealed heterogeneous responses and functional differentiation of hemocytes against white spot syndrome virus infection in Litopenaeus vannamei .

  • Authors : Cui C; Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, China.; Tang X

Subjects: Arthropod Proteins*/Arthropod Proteins*/Arthropod Proteins*/genetics ; Hemocytes*/Hemocytes*/Hemocytes*/cytology ; Hemocytes*/Hemocytes*/Hemocytes*/immunology

  • Source: Journal of virology [J Virol] 2024 Mar 19; Vol. 98 (3), pp. e0180523. Date of Electronic Publication: 2024 Feb 07.Publisher: American Society For Microbiology Country of Publication: United States NLM ID: 0113724 Publication Model: Print-Electronic Cited Medium:

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Academic Journal

Integration of scRNA-seq data by disentangled representation learning with condition domain adaptation.

  • Authors : Liu R; School of Mathematics and Physics, China University of Geosciences (Wuhan), Wuhan, 430074, China.; Qian K

Subjects: Single-Cell Gene Expression Analysis* ; Learning*; Cluster Analysis

  • Source: BMC bioinformatics [BMC Bioinformatics] 2024 Mar 16; Vol. 25 (1), pp. 116. Date of Electronic Publication: 2024 Mar 16.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105

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Academic Journal

Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform.

  • Authors : Nagai LAE; Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo 113-0032, Japan. Electronic address: .; Lee S

Subjects: Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; Software*; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: STAR protocols [STAR Protoc] 2024 Mar 15; Vol. 5 (1), pp. 102926. Date of Electronic Publication: 2024 Mar 10.Publisher: Cell Press Country of Publication: United States NLM ID: 101769501 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Protocol to dissect and dissociate the mouse brainstem for single-cell RNA-seq applications.

  • Authors : Phillips WS; Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden. Electronic address: .

Subjects: Single-Cell Gene Expression Analysis* ; Brain Stem*; Mice

  • Source: STAR protocols [STAR Protoc] 2024 Mar 15; Vol. 5 (1), pp. 102908. Date of Electronic Publication: 2024 Mar 08.Publisher: Cell Press Country of Publication: United States NLM ID: 101769501 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Determination of internal controls for quantitative gene expression of Spodoptera litura under microbial pesticide stress.

  • Authors : Wu S; Institute of Vegetable and Flower Research, Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.; Luo Y

Subjects: Gene Expression Profiling* ; Actins*/Actins*/Actins*/genetics; Animals

  • Source: Scientific reports [Sci Rep] 2024 Mar 13; Vol. 14 (1), pp. 6143. Date of Electronic Publication: 2024 Mar 13.Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

De novo transcriptomic analysis of Doum Palm (Hyphaene compressa) revealed an insight into its potential drought tolerance.

  • Authors : Borlay AJ; Department of Biological Sciences, University of Liberia, Monrovia, Liberia.; Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation, Nairobi, Kenya.

Subjects: Drought Resistance* ; Gene Expression Profiling*; Humans

  • Source: PloS one [PLoS One] 2024 Mar 12; Vol. 19 (3), pp. e0292543. Date of Electronic Publication: 2024 Mar 12 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet

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Academic Journal

scFSNN: a feature selection method based on neural network for single-cell RNA-seq data.

  • Authors : Peng M; School of Mathematical Sciences, Shenzhen University, Nanshan, Shenzhen, 518060, Guangdong, China.; School of Mathematics and Statistics and KLAS, Northeast Normal University, Renmin Street, Changchun, 130000, Jilin, China.

Subjects: Single-Cell Gene Expression Analysis* ; Neural Networks, Computer*; Computer Simulation

  • Source: BMC genomics [BMC Genomics] 2024 Mar 08; Vol. 25 (1), pp. 264. Date of Electronic Publication: 2024 Mar 08.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164

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Academic Journal

Principled and interpretable alignability testing and integration of single-cell data.

  • Authors : Ma R; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115.; Sun ED

Subjects: Algorithms* ; Gene Expression Profiling*; Gene Expression

  • Source: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2024 Mar 05; Vol. 121 (10), pp. e2313719121. Date of Electronic Publication: Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet

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Academic Journal

Improving gene set enrichment analysis (GSEA) by using regulation directionality.

  • Authors : Wang B; Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.; van der Kloet F

Subjects: Gene Expression Profiling* ; Transcriptome*; Transcription Factors

  • Source: Microbiology spectrum [Microbiol Spectr] 2024 Mar 05; Vol. 12 (3), pp. e0345623. Date of Electronic Publication: 2024 Jan 31.Publisher: ASM Press Country of Publication: United States NLM ID: 101634614 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework.

  • Authors : Zhan X; Department of Intelligence Engineering, College of Artificial Intelligence, Nankai University, Tianjin 300350, China.; Yin Y

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Mar 04; Vol. 40 (3).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

Validation of RNA Extraction Methods and Suitable Reference Genes for Gene Expression Studies in Developing Fetal Human Inner Ear Tissue.

  • Authors : Steinacher C; Department of Otorhinolaryngology, Medical University Innsbruck, 6020 Innsbruck, Austria.; Rieder D

Subjects: RNA* ; Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods; Humans

  • Source: International journal of molecular sciences [Int J Mol Sci] 2024 Mar 02; Vol. 25 (5). Date of Electronic Publication: 2024 Mar 02.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Academic Journal

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets.

  • Authors : Li K; College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University.; Fan Y

Subjects: Transcriptome* ; Gene Expression Profiling*; Gene Expression Regulation

  • Source: Journal of visualized experiments : JoVE [J Vis Exp] 2024 Mar 01 (205). Date of Electronic Publication: 2024 Mar 01.Publisher: MYJoVE Corporation Country of Publication: United States NLM ID: 101313252 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data.

  • Authors : Osorio D; Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA. .; Capasso A

Subjects: Gene Regulatory Networks* ; Gene Expression Regulation*; Humans

  • Source: Nature computational science [Nat Comput Sci] 2024 Mar; Vol. 4 (3), pp. 237-250. Date of Electronic Publication: 2024 Mar 04.Publisher: Springer Nature Country of Publication: United States NLM ID: 101775476 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses.

  • Authors : Shokri-Gharelo R; Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran; Researcher of Sugar Beet Seed Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran. Electronic address: .

Subjects: Triticum*/Triticum*/Triticum*/genetics ; Gene Expression Regulation, Plant*/Gene Expression Regulation, Plant*/Gene Expression Regulation, Plant*/genetics; Gene Expression Profiling

  • Source: Bio Systems [Biosystems] 2024 Mar; Vol. 237, pp. 105165. Date of Electronic Publication: 2024 Feb 29.Publisher: Elsevier Science Ireland Country of Publication: Ireland NLM ID: 0430773 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Comprehensive RNA-sequencing analysis of colorectal cancer in a Korean cohort.

  • Authors : Lee J; Department of Surgery, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Uijeongbu 11765, Republic of Korea. Electronic address: .; Kim JH

Subjects: Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; Colorectal Neoplasms*/Colorectal Neoplasms*/Colorectal Neoplasms*/metabolism; Humans

  • Source: Molecules and cells [Mol Cells] 2024 Mar; Vol. 47 (3), pp. 100033. Date of Electronic Publication: 2024 Feb 23.Publisher: Elsevier Country of Publication: United States NLM ID: 9610936 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm.

  • Authors : Pappas MP; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA.; Kawakami H

Subjects: Gene Expression Regulation, Developmental* ; Mesoderm*/Mesoderm*/Mesoderm*/metabolism ; DNA-Binding Proteins*/DNA-Binding Proteins*/DNA-Binding Proteins*/metabolism

  • Source: Development (Cambridge, England) [Development] 2024 Mar 01; Vol. 151 (5). Date of Electronic Publication: 2024 Mar 04.Publisher: Company Of Biologists Limited Country of Publication: England NLM ID: 8701744 Publication Model: Print-Electronic Cited Medium: Internet

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Academic Journal

Building flexible and robust analysis frameworks for molecular subtyping of cancers.

  • Authors : Pedersen CB; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.; Center for Genomic Medicine, Rigshospitalet - Copenhagen University Hospital, Denmark.

Subjects: Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; Breast Neoplasms*/Breast Neoplasms*/Breast Neoplasms*/diagnosis ; Breast Neoplasms*/Breast Neoplasms*/Breast Neoplasms*/genetics

  • Source: Molecular oncology [Mol Oncol] 2024 Mar; Vol. 18 (3), pp. 606-619. Date of Electronic Publication: 2024 Jan 07.Publisher: John Wiley & Sons, Inc Country of Publication: United States NLM ID: 101308230 Publication Model: Print-Electronic Cited Medium: Internet

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Academic Journal

Comprehensive scRNA-seq Model Reveals Artery Endothelial Cell Heterogeneity and Metabolic Preference in Human Vascular Disease.

  • Authors : Zeng L; Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, People's Republic of China.; Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease (Army Medical University), Ministry of Education, Beijing, People's Republic of China.

Subjects: Gene Expression Profiling* ; Vascular Diseases*; Humans

  • Source: Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2024 Mar; Vol. 16 (1), pp. 104-122. Date of Electronic Publication: 2023 Nov 17.Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101515919 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

Combining Global-Constrained Concept Factorization and a Regularized Gaussian Graphical Model for Clustering Single-Cell RNA-seq Data.

  • Authors : Xu Y; School of Sciences, East China Jiaotong University, Nanchang, 330013, China.; Zhang W

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2024 Mar; Vol. 16 (1), pp. 1-15. Date of Electronic Publication: 2023 Oct 10.Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101515919 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Academic Journal

PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida.

  • Authors : Koh E; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.; Goh W

Subjects: Gene Expression Profiling* ; Arabidopsis*/Arabidopsis*/Arabidopsis*/genetics; Transcriptome/Transcriptome/Transcriptome/genetics

  • Source: The Plant journal : for cell and molecular biology [Plant J] 2024 Mar; Vol. 117 (5), pp. 1592-1603. Date of Electronic Publication: 2023 Dec 04.Publisher: Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology Country of Publication: England NLM ID:

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Academic Journal

Single-cell RNA-Seq reveals the earliest lineage specification and X chromosome dosage compensation in bovine preimplantation embryos.

  • Authors : Hu B; Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.; Jin H

Subjects: Single-Cell Gene Expression Analysis* ; Blastocyst*; Pregnancy

  • Source: FASEB journal : official publication of the Federation of American Societies for Experimental Biology [FASEB J] 2024 Feb 29; Vol. 38 (4), pp. e23492.Publisher: Federation of American Societies for Experimental Biology Country of Publication: United States NLM ID: 8804484 Publication Model: Print Cited

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Academic Journal

Quantifying the clusterness and trajectoriness of single-cell RNA-seq data.

  • Authors : Lim HS; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America.; Qiu P

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*; Sequence Analysis, RNA

  • Source: PLoS computational biology [PLoS Comput Biol] 2024 Feb 28; Vol. 20 (2), pp. e1011866. Date of Electronic Publication: 2024 Feb 28 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Academic Journal

A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization.

  • Authors : Monnier L; Paris-Saclay University, CentraleSupélec, Laboratory of Mathematics and Computer Science (MICS), Gif-sur-Yvette, France.; Cournède PH

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Humans

  • Source: PLoS computational biology [PLoS Comput Biol] 2024 Feb 22; Vol. 20 (2), pp. e1011880. Date of Electronic Publication: 2024 Feb 22 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Academic Journal

Chemical and Transcriptomic Analyses of Leaf Cuticular Wax Metabolism in Ammopiptanthus mongolicus under Osmotic Stress.

  • Authors : Sumbur B; Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China.; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China.

Subjects: Plant Leaves*/Plant Leaves*/Plant Leaves*/chemistry ; Gene Expression Profiling*; Osmotic Pressure

  • Source: Biomolecules [Biomolecules] 2024 Feb 16; Vol. 14 (2). Date of Electronic Publication: 2024 Feb 16.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X

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Academic Journal

Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE.

  • Authors : Lin Y; School of Mathematics and Statistics, The University of Sydney, NSW 2006, Australia.; Charles Perkins Centre, The University of Sydney, NSW 2006, Australia.

Subjects: Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Animals

  • Source: Genome research [Genome Res] 2024 Feb 07; Vol. 34 (1), pp. 119-133. Date of Electronic Publication: 2024 Feb 07.Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9518021 Publication Model: Electronic Cited Medium:

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Academic Journal

Transcriptomic and Metabolic Profiling Reveal the Mechanism of Ovule Development in Castanea mollissima .

  • Authors : Cui Y; College of Forestry, Beijing Forestry University, Beijing 100083, China.; State Key Laboratory of Efficient Production of Forest Resources, Beijing 100083, China.

Subjects: Ovule*/Ovule*/Ovule*/metabolism ; Gene Expression Profiling*; Ethylenes/Ethylenes/Ethylenes/metabolism

  • Source: International journal of molecular sciences [Int J Mol Sci] 2024 Feb 06; Vol. 25 (4). Date of Electronic Publication: 2024 Feb 06.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Academic Journal

Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes.

  • Authors : Company C; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany.; Schmitt MJ

Subjects: Gene Expression Regulation* ; DNA*; Animals

  • Source: Nature communications [Nat Commun] 2024 Feb 05; Vol. 15 (1), pp. 897. Date of Electronic Publication: 2024 Feb 05.Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN:

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Academic Journal

Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice.

  • Authors : Durkin SM; Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America.; Ballinger MA

Subjects: Gene Expression Regulation*/Gene Expression Regulation*/Gene Expression Regulation*/genetics ; Evolution, Molecular*; Animals

  • Source: PLoS genetics [PLoS Genet] 2024 Feb 02; Vol. 20 (2), pp. e1010892. Date of Electronic Publication: 2024 Feb 02 (Print Publication: 2024).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101239074 Publication Model: eCollection Cited Medium: Internet

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Academic Journal

[Identification and functional analysis of jasmonic acid signaling repressor McJAZ8 gene in Mentha canadensis].

  • Authors : Zhang GL; College of Agriculture, Sichuan Agricultural University Chengdu 611130, China.; Tang WL

Subjects: Gene Expression Profiling* ; Mentha* ; Cyclopentanes*

  • Source: Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica [Zhongguo Zhong Yao Za Zhi] 2024 Feb; Vol. 49 (3), pp. 691-701.Publisher: Zhongguo yao xue hui : Zhongguo Zhong yi yan jiu yuan Zhong yao yan jiu suo Country of Publication: China NLM ID: 8913656 Publication Model: Print

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Academic Journal

Phenotype prediction from single-cell RNA-seq data using attention-based neural networks.

  • Authors : Mao Y; School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.; Lin YY

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Humans

  • Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Feb 01; Vol. 40 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

Reference gene selection for quantitative real-time PCR analysis of Hymenopellis radicata under abiotic stress.

  • Authors : Cao L; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, Gansu, China.; Zhang Q

Subjects: Genes, Plant* ; Gene Expression Regulation, Plant* ; Agaricales*Hymenopellis radicata

  • Source: Fungal biology [Fungal Biol] 2024 Feb; Vol. 128 (1), pp. 1567-1577. Date of Electronic Publication: 2023 Nov 24.Publisher: Published by Elsevier, copyright by British Mycological Society Country of Publication: Netherlands NLM ID: 101524465 Publication Model:

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Academic Journal

A 19-Gene Signature of Serous Ovarian Cancer Identified by Machine Learning and Systems Biology: Prospects for Diagnostics and Personalized Medicine.

  • Authors : Kori M; Faculty of Health Sciences, Acibadem Mehmet Ali Aydinlar University, İstanbul, Türkiye.; Demirtas TY

Subjects: Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; Ovarian Neoplasms*/Ovarian Neoplasms*/Ovarian Neoplasms*/diagnosis ; Ovarian Neoplasms*/Ovarian Neoplasms*/Ovarian Neoplasms*/genetics

  • Source: Omics : a journal of integrative biology [OMICS] 2024 Feb; Vol. 28 (2), pp. 90-101. Date of Electronic Publication: 2024 Jan 29.Publisher: Mary Ann Liebert, Inc Country of Publication: United States NLM ID: 101131135 Publication Model: Print-Electronic Cited Medium: Internet

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Academic Journal

CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data.

  • Authors : Wang X; Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling 712100, China.; Chai Z

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Animals

  • Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Feb 01; Vol. 40 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification.

  • Authors : Zhu X; School of Computer and Information Security, Guangxi Key Laboratory of Trusted Software, Guilin University of Electronic Technology, Guilin 541004, China.; Meng S

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Feb 01; Vol. 40 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data.

  • Authors : Hsu CY; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, United States.; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37203, United States.

Subjects: Single-Cell Gene Expression Analysis* ; Single-Cell Analysis*; Sequence Analysis, RNA/Sequence Analysis, RNA/Sequence Analysis, RNA/methods

  • Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Feb 01; Vol. 40 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN:

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Academic Journal

FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data.

  • Authors : Koutrouli M; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark.; Nastou K

Subjects: Proteomics* ; Single-Cell Gene Expression Analysis*; Gene Expression Profiling

  • Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Feb 01; Vol. 40 (2).Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN:

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